This is an excellent paper showing a large dataset of nanoCT-scanned zircon grains to improve the alpha-ejection correction and eU concentration calculations for (U-Th)/He dating. This study uses and expands on their proven approach from a previous study on apatite. They find that 2D alpha-ejection corrections in zircon are fairly accurate when compared to 3D estimates. This is in contrast to their previous study in apatite which found significant differences between these approaches and proposed correction factors for 2D measurements. The authors provide a detailed analysis of their data and a rigorous assessment of the propagation of uncertainty to the calculated ages and eU concentrations. They also clearly lay out strategies and workflows for classifying grains and applying corrections, as well as assessing and propagating uncertainties. This study will be helpful to users of the (U-Th)/He method and can provide a template for sample processing workflows to help standardize these procedures between different laboratories. As such, it is a perfect fit for GChron.

Overall, this manuscript is well-written and organized, and the text and figures are presented in a highly polished form. The methodological approach, data analysis, and recommendations are well-documented in the main manuscript as well as the appendices. The authors clearly incorporated the feedback received on a similar previous study into this manuscript. My comments below mainly concern minor formatting details that can be addressed in copy-editing, and would, in my opinion, not require any revisions. I, therefore, recommend this manuscript be accepted in its present form.

Detailed Comments:

Line 78: Do the numbers for the resolution (0.84-0.92 μm) refer to the voxel size or the smallest possible distance between two objects that can be resolved?

Table 1: The formatting makes it hard to read, especially the second column. It’s not immediately apparent which lines belong to which sample. I suggest adding horizontal lines or additional space to separate the rows from each other.

Line 399: Insert spaces between number and unit to make it consistent with the rest of the text: “100μm”  --> “100 μm”. Also change elsewhere (Figure C1, Line 138, etc.).

Lines 434-441: This might be beyond the scope of this paper to discuss, but I’m wondering how the 2D and 3D volume-derived masses would compare to ICP-MS-derived Zr-based masses for zircon grains. Some labs measure Zr routinely and use that for calculating grain mass (e.g. Guenthner et al., 2016, G3). Using those two approaches concurrently could be used to derive the average density of the zircon grains, which correlates to the amount of crystal damage. The difference in density between pristine and highly metamict zircons of around 16% (as mentioned in Line 530) should be resolvable given the uncertainties mentioned in this manuscript.

This is a very nice contribution that aims to assess systematic errors and uncertainties of alpha-ejection corrections and eU determinations that stem from commonly used “2D” microscopy measurements by comparing a series of measurables derived from high-resolution nano-CT “3D” data and the conventional “2D” data. The authors did an excellent job in providing rich information regarding the overall approaches they used including sample selection, data acquisition, and statistical analyses. The conclusions made by the study are important for users of the ZHe method in offering quantified potential errors and additional uncertainties of conventional data and a retro-applicable geometric correction method. I find both the significance and quality of this work fit the scope of GChron, and I highly recommend publication with only minor revisions or clarification. Below I illustrated a few minor concerns/confusions, followed by line-specific comments.

In section 3.2, the authors assumed a zircon Th/U ratio of 0.87 and no Sm contribution owing to a lack of parent isotope measurements. Is it possible to perform some kind of supplementary analysis or offer more reasoning to demonstrate that the use of the assumed values (as opposed to sample-specific parent isotope measurements) would not lead to a significant difference in a series of calculated results presented later, nor the major conclusion?

The collapsed clarity dimension. I do enjoy reading the discussions of how zircon clarify is related to eU, which is a critical proxy for radiation damage accumulation and annealing, and the density of zircon. However, I am a little confused about the way the authors delivered their reasonings about abandoning the clarity dimension in the GEM (section 2.4, around lines 160-168). My understanding is that the manuscript is centered on the assessment of error and uncertainty in zircon dimensions, therefore one should be able to exclude the contribution of clarity in terms of the role of varying eU before performing analyses. However, as the author pointed out, zircon clarity is also related to its density, so I think this part of the role of zircon clarity should only be either retained or abandoned after showcasing the analyses presented later on. Therefore, does it make more sense to not abandon this dimension at this point of the manuscript?  Moving on, it seems that the authors use 1, 2, or 3 as a numerical index for grain clarity if I understood correctly. Could the clarity be treated as a continuum (through some methods like a grayscale image?) and would a different conclusion on the importance of grain clarity?

Line 78: Is there a reason that the resolution of the CT data is presented as a range? I am not sure if additional information is beneficial though. Regardless, at this scale, would it make sense to simplify it as ~1 µm for ease of reading?

Line 100: Table 1 might look clearer if (1) more space is allowed between rows separating different sample suites or (2) adapting a similar formatting to tables 2-4.

Line 138: additional space between number and unit.

Line 179-181: Minor comment. The first sentence of section 3.1 is a bit repetitive.  However, this starting sentence, whether or not in a revised form, seems to be a more explicit way to introduce the first-order goal of this study if placed in the Intro section.

Line 266-268: Would it be better if the definition of the corrections for systematic error could be more explicitly defined here? (e.g., incorporate details from Table 2 footnotes).

This manuscript by Zeigler and co-authors examines discrepancies between 2D (microscopy) and 3D (nanoCT) computed geometries in zircon grains. Zircon geometric measurements propagate into a number of different metrics (volume, alpha-ejection correction, eU concentration) that are important for generating and interpreting zircon (U-Th)/He data sets. I found the article to be very well written, the data to be high quality, and the scope to be appropriate for the readership at Geochronology. I have three general comments. I would suggest that addressing the first one would encompass some new calculations from existing data. The other two could largely be addressed with additional discussion text. As such, I think these are “moderate” revisions.

• I am wondering how the Ft error would be different if a different set of 2D geometry equations were used. Both Hourigan et al. (2005, https://doi.org/10.1016/j.gca.2005.01.024) and Reiners et al. (2005, American Journal of Science v. 305, p. 259-311) derive a set of Ft equations that take into the account the specific dimensions of the two pyramidal terminations in a given zircon grain. Specifically, see equations 1-3 in the Reiners et al. (2005) article. The Ketcham et al. (2011) equations do take the pyramid heights into account, but only as a uniform approximation, whereas the Hourigan et al. equations, further derived by Reiners et al., are grain specific. My question then is, is the magnitude of the errors that result from the 2D and 3D comparison of volume and Ft in figure 7 somewhat mitigated by using equations that incorporate metrics for the terminations? The authors seem to suggest as much at line 390. I would encourage the authors to examine this by measuring tip heights directly from their collected images. This is significant in so far as the authors are proposing a general correction that could be applied to previously published datasets, and I know from experience that all zircon (U-Th)/He data sets generated at the University of Arizona (of which there are a bunch in the published literature at this point) use the Reiners et al. (2005) correction and not the Ketcham et al. (2011).

• There is little mention in the current version of the manuscript concerning U and Th zonation and its influence on the Ft correction. The authors have defined the scope of the current work to focus on corrections to potential systematic error introduced by relying on a 2D geometric approximation only, and this is fine and appropriate. A full consideration of this influence plus the zonation effect would likely be a separate study. However, again, given that the authors propose a general-use error assignment for all zircon grains with only 2D measurements, my concern is that this correction could still give false confidence in what the actual, true Ft error correction should be. For example, common scenarios of U and Th zonation in zircon can lead to Ft correction errors of ~30 % (Hourigan et al., 2005), which is far greater than the errors discussed here. How do the authors consider their findings in comparison to those of Hourigan et al. (2005) and their recommendations for Ft error correction? Zonation is admittedly a pernicious issue, and so there might not be a great answer to this question without resorting to time-intensive in situ approaches, but the authors do need to elaborate more on the error discrepancies here.

• How do the results here compare with the Zr stoichiometric approach of Guenthner et al. (2016)? A comparison of Figure 4a in Guenthner et al. (2016) and Figure 7a seems to suggest that there might be good first-order agreement between the 3D approach and the stoichiometric approach. Have these zircon grains already been dissolved? A useful follow-up would be a direct comparison among the 3D, 2D, and stoichiometric approach. This is likely outside the scope of the current study, but some additional discussion along these lines is warranted in the current text.

Willy Guenthner

UIUC